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4,753 results for “SHAPE”
On this side of the fence: Functional responses to linear landscape features shape the home range of large herbivores
<p>1. Understanding the consequences of global change for animal movement is a major issue for conservation and management. In particular, habitat fragmentation generates increased densities of linear landscape features that can impede movements.</p> <p>2. While the influence of these features on animal movements has been intensively investigated, they may also play a key role at broader spatial scales (e.g. the home range scale) as resources, cover from predators/humans, corridors/barriers, or landmarks. How space use respond to varying densities of linear features has been mostly overlooked in large herbivores, in contrast to studies done on predators. Focusing on large herbivores should provide additional insights to understand how animals solve the trade-off between energy acquisition and mortality risk.</p> <p>3. Here, we investigated the role of anthropogenic (roads and tracks) and natural (ridges, valley bottoms and forest edges) linear features on home range features in five large herbivores. We analysed an extensive GPS monitoring data base of 696 individuals across nine populations, ranging from mountain areas mostly divided by natural features to lowlands that were highly fragmented by anthropogenic features.</p> <p>4. Nearly all of the linear features studied were found at the home range periphery, suggesting that large herbivores primarily use them as landmarks to delimit their home range. In contrast, for mountain species, ridges often occurred in the core range, probably related to their functional role in terms of resources and refuge. When the density of linear features was high, they no longer occurred predominantly at the home range periphery, but instead were found across much of the home range. We suggest that, in highly fragmented landscapes, large herbivores are constrained by the costs of memorising the spatial location of key features, and by the requirement for a minimum area to satisfy their vital needs.</p> <p>5. These patterns were mostly consistent in both males and females and across species, suggesting that linear features have a preponderant influence on how large herbivores perceive and use the landscape.</p>
Spatial autocorrelation shapes liana distribution better than topography and host tree properties in a subtropical evergreen broadleaved forest in SW China
<p>Lianas are an important component of subtropical forests, but the mechanisms underlying their spatial distribution patterns have received relatively little attention. Here, we selected 12 most abundant liana species, constituting up to 96.9% of the total liana stems, in a 20-ha plot in a subtropical evergreen broadleaved forest at 2,472 – 2,628 m elevation in SW China. Combining data on topography (convexity, slope, aspect, and elevation) and host trees (density and size) of the plot, we addressed how liana distribution is shaped by host tree properties, topography and spatial autocorrelation by using principal coordinates of neighbor matrices (PCNM) analysis. We found that lianas had an aggregated distribution based on the Ripley's <i>K</i> function. At the community level, PCNM analysis showed that spatial autocorrelation explained 43% variance in liana spatial distribution. Host trees and topography explained 4% and 18% of the variance, but less than 1% variance after taking spatial autocorrelation into consideration. A similar trend was found at the species level. These results indicate that spatial autocorrelation might be the most important factor shaping liana spatial distribution in subtropical forest at high elevation.</p>
Density-by-diet interactions during larval development shape adult life-history trait expression and fitness in a polyphagous fly
<p><span>Habitat quality early in life determines individual fitness, with possible long-term evolutionary effects on groups and populations. In holometabolous insects, larval ecology plays a major role in determining the expression of traits in adulthood, but how ecological conditions during larval stage interact to shape adult life-history and fitness, particularly in non-model organisms, remains subject to scrutiny. Consequently, our knowledge of the interactive effects of ecological factors on insect development is limited. Here, using the polyphagous fly <i>Bactrocera tryoni</i>, we conducted a fully-factorial design where we manipulated larval density and larval diet (protein-rich, standard, and sugar-rich) to gain insights into how these ecological factors interact to modulate adult fitness. As expected, a protein-rich diet resulted in faster larval development, heavier and leaner adults that were more fecund compared with standard and sugar-rich diets, irrespective of larval density. Females from the protein-rich larval diet had overall higher reproductive rate (i.e., eggs per day) than females from other diets, and reproductive rate decreased linearly with density for females from the protein-rich but non-linearly for females from the standard and sugar-rich diets over time. Surprisingly, adult lipid reserve increased with larval density for adults from the sugar-rich diet (as opposed to decreasing, as in other diets), possibly due to a stress-response to an extremely adverse condition during development (i.e., high intraspecific competition and poor nutrition). Together, our results provide insights into how ecological factors early in life interact and shape the fate of individuals through life-stages in holometabolous insects. </span></p>
MicroED data collected from ribbon-shaped (originally thought to be needle-shaped) orthorhombic lysozyme crystals (2016-2017)
<p>Raw data used in the following journal article:</p> <p>Xu et al., 2018, Structure26, 667–675</p> <p>https://doi.org/10.1016/j.str.2018.02.015</p> <p>Information of the data is included in the ReadME.pdf</p>
Economic and not ecological variables shape the sparing-sharing trade-off in a mixed cropping landscape
<p>1. The framework of land sparing vs. land sharing provides a useful analytical tool to address the crop-production/biodiversity trade-off. Despite multiple case-studies testing the sparing-sharing trade-off, this framework still lacks the ability to identify the conditions in which sparing, or sharing, would be the preferred strategy for pareto-optimizing both food-production and biodiversity. Under some conditions, ecosystem services may create a positive feedback between biodiversity and crop production, affecting the optimization.</p> <p>2. This study aims to identify the conditions and the relevant variables that determine the preferred land-use strategy in terms of maximizing both biodiversity and food production, while accounting for positive feedback of ecosystem services in this analysis. We used a simulation model with data from a mixed cropping landscape (100 km<sup>2</sup>) covering seven crop types, five taxonomic groups, three biodiversity metrics and 23 bioindicators to explore the variables shaping the biodiversity-production trade-off and ecosystem services underlying it. We explored a continuum of sparing large semi-natural patches to sharing by maintaining uncultivated field margins of varying size.</p> <p>3. Land sparing outperformed land sharing in 62% of the scenarios and it was economically more predictable. The optimization was shaped by costs, associated with crop type, rather than by landscape composition and configuration, biodiversity metric, taxonomic group or bioindicator.</p> <p>4. Landscape configuration and taxonomic group results corroborate the notion that land sharing benefits mainly small organisms, and that the common width of field-margins in many agri-environmental policies (10 m) is not cost-effective compared to land sparing.</p> <p>5. Land sharing was the optimal strategy whenever it resulted in minimal costs, despite contributing little to biodiversity. Yet, when field margins were >20 m wide (small-scale sparing), land sharing maintained higher biodiversity and was at least as cost-effective as sparing.</p> <p>6. <em>Synthesis and applications</em>. Our model highlights the importance of socio-economic variables compared to ecological variables in selecting land-management strategy to pareto-optimize both food production and biodiversity. Considering opportunity costs alongside economic benefits from ecosystem services in various cropping systems may therefore improve the cost-effectiveness of biodiversity conservation policies in agricultural landscapes.</p>
Optimizing Within-Distance Queries by Approximating Shapes with Maximal Bounded Boxes - Datasets
<p>Csv and sql files for the underlying data.<br> Figure 9: Calculating the distance between various number and type of shapes, i.e. from polygons, rotated and axis aligned rectangles, to points, polygons, rotated and axis aligned rectangles.<br> Table 1: Calculating distance between shapes of various complexity, i.e. points, lines, quadrilaterals, hexagons, dodecagons, icosagons, pentacontagons.<br> Table 2: Comparing the ordering of the shapes when distance operation is calculated, (a) from polygons to rectangles, (b) from rectangles to polygons.<br> Table 5 & 6: Within-distance and distance queries between (a) actual polygons, (b) their bounded rectangles, (c) actual polygons and points, (d) their bounded rectangles and points.</p>
Female reproductive mode shapes allometric scaling of male traits in livebearing fishes (family Poeciliidae)
<p>Reproductive mode is predicted to influence the form of sexual selection. The viviparity driven conflict hypothesis posits that a shift from lecithotrophic (yolk-nourished) to matrotrophic (mother-nourished or placental) viviparity drives a shift from pre-copulatory toward post-copulatory sexual selection. In lecithotrophic species, we predict that pre-copulatory sexual selection will manifest as males exhibiting a broad distribution of sizes, and small and large males exhibiting contrasting phenotypes (morphology and coloration); conversely, in matrotrophic species an emphasis on post-copulatory sexual selection will preclude these patterns. We test these predictions by gathering data on male size, morphology, and coloration for five sympatric Costa Rican poeciliid species that differ in reproductive mode (i.e. lecithotrophy vs matrotrophy). We find tentative support for these predictions of the viviparity driven conflict hypothesis, with some interesting caveats and subtleties. In particular, we find that the three lecithotrophic species tend to show a broader distribution of male sizes than matrotrophic species. Furthermore, large males of such species tend to exhibit proportionately large dorsal and caudal fins and short gonopodia relative to small males, while these patterns are expressed to a lesser extent in the two matrotrophic species. Finally, large males in some of the lecithotrophic species exhibit darker fins relative to small males, a pattern not evident in either matrotrophic species. One unexpected finding was that even in the matrotrophic species <i>Poeciliopsis retropinna</i> and <i>Poeciliopsis paucimaculata</i>, which lack courtship and dichromatic coloration, some morphological traits exhibit significant allometric relationships, suggesting that even in these species pre-copulatory sexual selection may be present and shaping size-specific male phenotypes in subtle ways.</p>
The sense of body ownership shapes the visual representation of body size
<p>Data collected and analyzed in the manuscript: Giurgola S, Crico C, Farnè A, Bolognini N. The sense of body ownership shapes the visual representation of body size. J Exp Psychol Gen. 2021 Oct 25. doi: 10.1037/xge0001111; PMID: 34694859.</p>
FIGURE. Multiclavula caput-serpentis (KaiR699, holotype). a. Embankment covered by the thallus, with several groups of numerous basidiocarps (arrows). b. Thallus on soil, with a group of basidiocarps. c. Basidiocarps with different shapes, +/- lateral view. d. Basidiocarps from below-lateral. Bars a = 20 cm, b = 1 cm, c, d = 2 mm. Photos by K. Reschke. in New and interesting species of Agaricomycetes from Panama
FIGURE. Multiclavula caput-serpentis (KaiR699, holotype). a. Embankment covered by the thallus, with several groups of numerous basidiocarps (arrows). b. Thallus on soil, with a group of basidiocarps. c. Basidiocarps with different shapes, +/- lateral view. d. Basidiocarps from below-lateral. Bars a = 20 cm, b = 1 cm, c, d = 2 mm. Photos by K. Reschke.
Dataset - Low-hysteresis shape-memory ceramics designed by multimode modelling
<p>Accompanying Dataset for the article "Low-hysteresis shape-memory ceramics designed by multimode modelling". The dataset contains two .csv files, one each for tetragonal and monoclinic phase, containing lattice parameter data used to train the ML models. Lattice parameters are in angstroms, compositions are in mole percent (cation site), temperatures are in degrees Celsius.</p>
Demographic history has shaped the strongly differentiated corkwing wrasse populations in Northern Europe
<p>Understanding the biological processes involved in genetic differentiation and divergence between populations within species is a pivotal aim in evolutionary biology. One particular phenomenon that requires clarification is the maintenance of genetic barriers despite the high potential for gene flow in the marine environment. Such patterns have been attributed to limited dispersal or local adaptation, and to a lesser extent to the demographic history of the species. The corkwing wrasse (<i>Symphodus melops</i>) is an example of a marine fish species where regions of particular strong divergence are observed. One such genetic break occurred at a surprisingly small spatial scale (<i>F</i><sub>ST</sub> ~0.1), over a short coastline (<60 km) in the North Sea-Skagerrak transition area in southwestern Norway. Here, we investigate the observed divergence and purported reproductive isolation using genome resequencing. Our results suggest that historical events during the post-glacial recolonization route can explain the present population structure of the corkwing wrasse in the northeast Atlantic. While the divergence across the break is strong, we detected ongoing gene flow between populations over the break suggesting recent contact or negative selection against hybrids. Moreover, we found few outlier loci and no clear genomic regions potentially being under selection. We concluded that neutral processes and random genetic drift e.g., due to founder events during colonization have shaped the population structure in this species in Northern Europe. Our findings underline the need to take into account the demographic process in studies of divergence processes.</p>
Fig. 2. Head sculpture and femora shapes. A, C in A revision of the Afrotropical species of the Dorylinae ant genus Aenictus (Hymenoptera: Formicidae) based on the worker caste
Fig. 2. Head sculpture and femora shapes. A, C, Aenictus guineensis (CASENT0876634). B, Aenictus xegi sp. nov. (NHMUK012849243). D, Aenictus susanae sp. nov. (CASENT0406729).
Fig. 1. Mandibular and clypeal shapes for the different species groups. A in A revision of the Afrotropical species of the Dorylinae ant genus Aenictus (Hymenoptera: Formicidae) based on the worker caste
Fig. 1. Mandibular and clypeal shapes for the different species groups. A, gr. rotundatus (Aenictus guineensis, CASENT0876634). B, gr. koloi (Aenictus koloi, sp. nov., KGCOL00552). C, gr. eugenii (Aenictus eugenii, CASENT0235822). D, gr. eugenii (Aenictus mvuvii, sp. nov., CASENT0350555). E, gr. popeyei (Aenictus popeyei, sp. nov., CASENT0810234). F, gr. decolor (Aenictus decolor, CASENT0317077). G, gr. asantei (Aenictus asantei, NHMUK012849241). H, gr. rixator (Aenictus rixator, CASENT0907030).
Script and data used in: A lot of convergence, a bit of divergence: environment and interspecific interactions shape body color patterns in Lissotriton newts
<p>Coexistence with related species poses evolutionary challenges to which populations may react in diverse ways. When exposed to similar environments, sympatric populations of two species may adopt similar phenotypic trait values. However, selection may also favor trait divergence as a way to reduce competition for resources or mates. The characteristics of external body parts, such as coloration and external morphology, are involved to varying degrees in intraspecific signaling as well as in the adaptation to the environment, and consequently may be diversely affected by interspecific interactions in sympatry. Here, we studied the effect of sympatry on various color and morphological traits in males and females of two related newt species <i>Lissotriton helveticus</i> and <i>L. vulgaris</i>. Importantly, we did not only estimate how raw trait differences between species respond to sympatry, but also the marginal responses after controlling for environmental variation. We found that dorsal and caudal coloration converged in sympatry, likely reflecting their role in adaptation to local environments, especially concealment from predators. In contrast, aspects of male and female ventral coloration, which harbours sexual signals in both species, diverged in sympatry. This divergence may reduce opportunities for interspecific sexual interactions and the associated loss of energy, suggesting reproductive character displacement (RCD). Our study emphasizes the contrasting patterns of traits involved in different functions and calls for the need to consider this diversity in evolutionary studies.</p>
The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex
<p>Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, <i>Daphnia pulicaria </i>and <i>Daphnia pulex. </i>First, we assembled a phased chromosome-scale genome assembly using trio-binning for <i>D. pulicaria</i> and constructed a genetic map using an F2-intercross panel to understand sex-specific recombination rate heterogeneity.<i> </i>Finally, we used a ddRADseq dataset with broad geographic sampling of <i>D. pulicaria, D. pulex, </i>and their hybrids to understand the patterns of genome-scale divergence and demographic parameters. Our study provides the first sex-specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male-biased heterochiasmy in <i>D. pulicaria</i>, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are likely driven by selection on <i>D. pulicaria</i>, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome-wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.</p>
On the shape-dependent propulsion of nano- and microparticles by traveling ultrasound waves
<p>Supplementary data for the following manuscript: Johannes Voß, Raphael Wittkowski, "On the shape-dependent propulsion of nano- and microparticles by traveling ultrasound waves ", <em><strong>Nanoscale Adv.</strong></em>, 2020,<strong>2</strong>, 3890-3899, doi=10.1039/D0NA00099J</p>
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants. in Phylogenetic approach for identification and life cycles of Puccinia (Pucciniaceae) species on Poaceae from northeastern China
FIGURE. Phylogenetic tree of specimens on Poaceae and related host plants constructed by MP method based on ITS+28S regions of rDNA. Bootstrap values of MP and ML are followed by the Bayesian posterior probabilities (Bpp) on the nodes in the topology. Asterisk (*) represents bootstrap values or Bpp less than 50% in the topology. Sample data are shown with voucher specimen number or GenBank accession number, and host plant. Sequence data determined in this study are shown in color. Teliospore shapes are shown in each clade detected, and new species are shown by asterisk (*) on clades. 0, I: Spermogonial and aecial host genus. Asterisk (*) on host plants: Spermogonial and aecial host plants.
Morphometric variations in cephalothorax shape of Whip Spiders
<p>Factor loadings for the ACP performed in the paper.</p>
Morphometric variations in cephalothorax shape of Whip Spiders
<p>Photographs of the specimens used.</p>
Dataset for: Body size and sexual selection shaped the evolution of parrot calls
<p><span>Morphology, habitat and various selective pressures (e.g., social and sexual selection) can influence the evolution of acoustic signals, but the relative importance of their effects is not well understood. The order Psittaciformes (parrots, <em>sensu lato</em>) is a large clade of very vocal and often gregarious species for which large-scale comparative studies of vocalizations are lacking. We measured acoustic traits (duration, sound frequency, frequency bandwidth and sound entropy) of the predominant call type for >200 parrot species to test: (1) for associations with body size; (2) the acoustic adaptation hypothesis (predicting differences between forest and open-habitat species); (3) the social complexity hypothesis (predicting more complex calls in gregarious species); and (4) influences of sexual selection (predicting correlated evolution with colour ornamentation). Larger species had on average longer calls, lower sound frequency and wider frequency bandwidth. These associations with body size are all predicted by physical principles of sound production. We found no evidence for the acoustic adaptation and social complexity hypotheses, but perhaps social complexity is associated with vocal traits not studied here, such as call repertoire sizes. More sexually dichromatic species had on average simpler calls (shorter, with lower entropy and narrower frequency bandwidth) indicating an influence of sexual selection, namely an evolutionary negative correlation between colour ornamentation and elaborate acoustic signals, as predicted by the transference hypothesis. Our study is the first large-scale attempt at understanding acoustic diversity across the Psittaciformes, and indicates that body size and sexual selection influenced the evolution of species differences in vocal signals.</span></p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.